binaries/src/muscle/fastclust.cpp

   1 #include "muscle.h"\r
   2 #include "seqvect.h"\r
   3 #include "distfunc.h"\r
   4 #include "clust.h"\r
   5 #include "clustsetdf.h"\r
   6 #include "tree.h"\r
   7 #include "clust.h"\r
   8 #include "distcalc.h"\r
   9 #include <math.h>\r
  10 \r
  11 static void TreeFromSeqVect_NJ(const DistFunc &DF, CLUSTER Cluster, Tree &tree)\r
  12         {\r
  13     ClustSetDF CSD(DF);\r
  14 \r
  15     Clust C;\r
  16     C.Create(CSD, Cluster);\r
  17 \r
  18     tree.FromClust(C);\r
  19         }\r
  20 \r
  21 static void TreeFromSeqVect_UPGMA(const DistFunc &DF, CLUSTER Cluster, Tree &tree)\r
  22         {\r
  23         LINKAGE Linkage = LINKAGE_Undefined;\r
  24         switch (Cluster)\r
  25                 {\r
  26         case CLUSTER_UPGMA:\r
  27                 Linkage = LINKAGE_Avg;\r
  28                 break;\r
  29         case CLUSTER_UPGMAMin:\r
  30                 Linkage = LINKAGE_Min;\r
  31                 break;\r
  32         case CLUSTER_UPGMAMax:\r
  33                 Linkage = LINKAGE_Max;\r
  34                 break;\r
  35         case CLUSTER_UPGMB:\r
  36                 Linkage = LINKAGE_Biased;\r
  37                 break;\r
  38         default:\r
  39                 Quit("TreeFromSeqVect_UPGMA, CLUSTER_%u not supported", Cluster);\r
  40                 }\r
  41         \r
  42         DistCalcDF DC;\r
  43         DC.Init(DF);\r
  44         UPGMA2(DC, tree, Linkage);\r
  45         }\r
  46 \r
  47 static void SaveDF(const SeqVect &v, DistFunc &d, const char *FileName)\r
  48         {\r
  49         FILE *f = fopen(FileName, "w");\r
  50         if (f == 0)\r
  51                 Quit("Cannot create %s", FileName);\r
  52 \r
  53         unsigned n = v.GetSeqCount();\r
  54         fprintf(f, "%u\n", n);\r
  55         for (unsigned i = 0; i < n; ++i)\r
  56                 {\r
  57                 fprintf(f, "%10.10s  ", v.GetSeqName(i));\r
  58                 for (unsigned j = 0; j < i; ++j)\r
  59                         fprintf(f, "  %9g", d.GetDist(i, j));\r
  60                 fprintf(f, "\n");\r
  61                 }\r
  62         fclose(f);\r
  63         }\r
  64 \r
  65 void TreeFromSeqVect(const SeqVect &v, Tree &tree, CLUSTER Cluster,\r
  66   DISTANCE Distance, ROOT Root, const char *SaveFileName)\r
  67         {\r
  68         DistFunc DF;\r
  69         DistUnaligned(v, Distance, DF);\r
  70         if (SaveFileName != 0)\r
  71                 SaveDF(v, DF, SaveFileName);\r
  72         if (CLUSTER_NeighborJoining == Cluster)\r
  73                 TreeFromSeqVect_NJ(DF, Cluster, tree);\r
  74         else\r
  75                 TreeFromSeqVect_UPGMA(DF, Cluster, tree);\r
  76         FixRoot(tree, Root);\r
  77         }\r